/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#ifndef PEPTIDEPMF_H
#define PEPTIDEPMF_H

#include <vector>

#include "peptide.h"
#include "modification.h"

/**
  A peptide plus some info only needed for pmf (which modif, and how much)


	@author Alexandre Masselot,,, <alex@alex-laptop>
*/
namespace bol{
class PeptidePMF : public Peptide
{
  vector<Modification*> m_vModif;
  vector<int> m_vNbModif;

public:
    PeptidePMF();
    PeptidePMF(const string seq):Peptide(seq){}


    ~PeptidePMF();


  void clearModif(){
    m_vModif.clear();
    m_vNbModif.clear();
  }

  

  /**
   * set the modif *m to appear n times
   * if this modif already exist on this peptide, it will simply be ignored. So you could have on the same peptide 2xOxidation and then 3xoxidation, which can be dangerous for PMF...
   * @param m a pointer to a defined modification
   * @param n integer (>0 or it should be somehow meaningless...)
   */
  void setModif(Modification* m, const int n);


  /**
   * add a modif (the counter will be incremented if it already exists)
   * @param m a pointer to a modification
   * @param n the number of time it counter must 
   */
  void addModif(Modification* m, const int n=1);

  double getMass()const;

  void setVModif(const vector< Modification * >& theValue) {
      m_vModif = theValue;
  }
  

  vector< Modification * > vModif() const {
      return m_vModif;
  }

  void setVNbModif(const vector< int >& theValue) {
      m_vNbModif = theValue;
  }
  

  vector< int > vNbModif() const {
      return m_vNbModif;
  }
  
  

};
}
#endif
